Periodic Reporting for period 1 - DNA-FAIRYLIGHTS (DNA-Fast light dRiven data technologY with multiplexed optical encoding and readout)
Periodo di rendicontazione: 2021-09-01 al 2022-08-31
Our hybrid metal nanoparticle/DNA will be developed for the encoding and reconfiguration (not read-only storage) of digital information at high density, combined with a fast and reliable method of data reading that avoids the time-consuming necessity to amplify the DNA for readout via sequencing. The development of such hybrid DNA systems will be a paradigm change for data encoding and storage, an area in which the current demand is rapidly outpacing the capabilities offered by semiconductor technologies. DNA-FAIRYLIGHTS will also establish a highly versatile material platform that will boost several other nanobiotechnology sectors, in particular high-resolution bio-imaging, steganography, encrypted information storage in manufacturing, extreme resolution patterning and tunable photonic/plasmonic systems.
• DNA-FAIRYLIGHTS will contribute to the development of new technologies for data storage based on nanomaterial assembly on a biomolecule template. Although DNA data storage technologies have been already demonstrated, their high cost, slow readout and read-only nature make them not applicable in the short/mid-term. The development of metallic nanoparticles (NPs) and ultrasmall light-emitting nanoclusters (NCs), together with their controlled assembly on not-synthetic DNA templates, will enable fast electro-optical reading of the encoded information by passing the functionalized strands through nanopores. This will be a milestone for future data storage, e.g. in the search for next generation methods for low cost and bioinspired digital data archiving, and together with the additional possibilities of reconfiguration (erase/rewrite), has the potential to radically transform the current approach in DNA data technology.
The overall objective of DNA-FAIRYLIGHTS is the development of a proof-of-concept platform for fast and inexpensive storage and manipulation of information on not-synthetic (biological) DNA. The use of distinct NPs and NCs enables to sequentially and directly identify the sequences of the encoded data from optical signals stemming from the specifically tailored nanostructures. This approach relies on two important aspects (Fig.1): A) A set of plasmonic NPs and light-emitting NCs consisting of different shapes and sizes provides several specific and well-defined resonances/transitions in the visible and near-infrared spectral range; B) their functionalization with a library of short oligonucleotide sequences that are complementary to specific sites in biological (not-synthetic) single stranded DNA, which enables controlled NP/NC decoration of the DNA strand. The decorated DNA will provide a reliable storage of information, but not less importantly, a direct strategy to read the stored information sequentially via the optical signal of the functionalized strand, thus without the need DNA amplification. We are introducing, for the first time in DNA data storage technology, the use of NPs and NCs as optical nanoresonators. This approach ensures a high degree of freedom in electromagnetic field engineering and, in particular, will permit the spectroscopic detection at discrete wavelengths of the encoded information. Here, the series of engineered optical resonances is defined by 9 different discrete elements that are used to decorate DNA molecules, resulting in a DNA hybrid system where a specific optical signal can be excited at discrete sites along the DNA strand. The size of the NPs / NCs, ranging from 1 up to 30 nm will require a radically new approach for the decoration of the DNA template. The short complementary oligos will consist of 20 base-pairs (bp) for the attachment to the DNA and will contain other sections for the linking to the NPs or NCs. Theoretically this concept enables to encode up to 420 (A, C, T, G) possible sequences for every NP / NC type, which represents a new paradigm with respect to the existing enzymatic DNA data storage.
• DNA-FAIRYLIGHTS will contribute to the development of new technologies for data storage based on nanomaterial assembly on a biomolecule template. Although DNA data storage technologies have been already demonstrated, their high cost, slow readout and read-only nature make them not applicable in the short/mid-term. The development of metallic nanoparticles (NPs) and ultrasmall light-emitting nanoclusters (NCs), together with their controlled assembly on not-synthetic DNA templates, will enable fast electro-optical reading of the encoded information by passing the functionalized strands through nanopores. This will be a milestone for future data storage, e.g. in the search for next generation methods for low cost and bioinspired digital data archiving, and together with the additional possibilities of reconfiguration (erase/rewrite), has the potential to radically transform the current approach in DNA data technology.
The overall objective of DNA-FAIRYLIGHTS is the development of a proof-of-concept platform for fast and inexpensive storage and manipulation of information on not-synthetic (biological) DNA. The use of distinct NPs and NCs enables to sequentially and directly identify the sequences of the encoded data from optical signals stemming from the specifically tailored nanostructures. This approach relies on two important aspects (Fig.1): A) A set of plasmonic NPs and light-emitting NCs consisting of different shapes and sizes provides several specific and well-defined resonances/transitions in the visible and near-infrared spectral range; B) their functionalization with a library of short oligonucleotide sequences that are complementary to specific sites in biological (not-synthetic) single stranded DNA, which enables controlled NP/NC decoration of the DNA strand. The decorated DNA will provide a reliable storage of information, but not less importantly, a direct strategy to read the stored information sequentially via the optical signal of the functionalized strand, thus without the need DNA amplification. We are introducing, for the first time in DNA data storage technology, the use of NPs and NCs as optical nanoresonators. This approach ensures a high degree of freedom in electromagnetic field engineering and, in particular, will permit the spectroscopic detection at discrete wavelengths of the encoded information. Here, the series of engineered optical resonances is defined by 9 different discrete elements that are used to decorate DNA molecules, resulting in a DNA hybrid system where a specific optical signal can be excited at discrete sites along the DNA strand. The size of the NPs / NCs, ranging from 1 up to 30 nm will require a radically new approach for the decoration of the DNA template. The short complementary oligos will consist of 20 base-pairs (bp) for the attachment to the DNA and will contain other sections for the linking to the NPs or NCs. Theoretically this concept enables to encode up to 420 (A, C, T, G) possible sequences for every NP / NC type, which represents a new paradigm with respect to the existing enzymatic DNA data storage.
During the first year of the project the consortium have worked on the set-up of all the basic experiments and models to enable the development of the DNA-data storage technology here proposed.
In particular, considering the separated contributions from the different partners:
-IIT, as coordinator, invested the first 12 months in the organization of the team, kick-off, people hiring, dissemination and communication activities (web-site, conferences, talks, etc). Moreover, IIT developed some preliminary methods for the fabrication of solid.state nanopores, as single and arrays. In collaboration with Elements, IIT developed an integrated device for the electrical characterization of the nanopores also with optical stimuli and implemented the set-up for the electro-optical measurements expected during the 2nd phase of the project
-ELE, in collaboration with IIT developed the basic system for the in-parallel electrical reading from nanopores and a device for optical-electrical control in nanopores
-CAM worked on the microfluici assembly of DNA+nanoparticles, also in collaboration with GUNE
-GUNE developed a new set of metallic nanoparticles and nanoclusters to be integrated / anchored on DNA template during the 2nd phase of the project (in collaboration with CAM, IIT and ABA)
-ETH and TUM started to theoretically investigate the error generation in DNA data storage based on the proposed method. Unfortunately, being not possible to far to use experimental data from nanopore reading, the major contributions are expected during the 2nd phase of the project
-STUTT developed, in collaboration with IIT and GUNE new systems for the controlled re-arrangement of metallic nanoparticles in DNA template with external stimuli
-DS and ABA, contributed, during this first year with some preliminary analyses, but the their major contributions are expected during the 2nd phase of the project
In particular, considering the separated contributions from the different partners:
-IIT, as coordinator, invested the first 12 months in the organization of the team, kick-off, people hiring, dissemination and communication activities (web-site, conferences, talks, etc). Moreover, IIT developed some preliminary methods for the fabrication of solid.state nanopores, as single and arrays. In collaboration with Elements, IIT developed an integrated device for the electrical characterization of the nanopores also with optical stimuli and implemented the set-up for the electro-optical measurements expected during the 2nd phase of the project
-ELE, in collaboration with IIT developed the basic system for the in-parallel electrical reading from nanopores and a device for optical-electrical control in nanopores
-CAM worked on the microfluici assembly of DNA+nanoparticles, also in collaboration with GUNE
-GUNE developed a new set of metallic nanoparticles and nanoclusters to be integrated / anchored on DNA template during the 2nd phase of the project (in collaboration with CAM, IIT and ABA)
-ETH and TUM started to theoretically investigate the error generation in DNA data storage based on the proposed method. Unfortunately, being not possible to far to use experimental data from nanopore reading, the major contributions are expected during the 2nd phase of the project
-STUTT developed, in collaboration with IIT and GUNE new systems for the controlled re-arrangement of metallic nanoparticles in DNA template with external stimuli
-DS and ABA, contributed, during this first year with some preliminary analyses, but the their major contributions are expected during the 2nd phase of the project
During the first year of the project, it has not been possible to achieve significant results beyond the state-of-the-art if we consider the goal of DNA data storage. On the contrary, as demonstrated by the different publications produced during this first year, several preliminary results, still beyond the state-of-the-art of their respective fields have been achieved.
In general, in the 2nd part of the project we expect more impactfull results. In particular, the highly interdisciplinary effort of DNA-FAIRYLIGHTS will lead to:
• development of advanced optical technologies based on NP and NC decorated (hybrid) DNA
• highly engineered systems for molecular functionalization
• Novel data encoding concepts based on multiplexed signals
• robust optical spectroscopic platform for single molecule reading based on solid-state nanopore arrays
• integration of the above technologies within a core multifunctional platform and
• iterative refinement of the data analysis based on assessment of instrument performance.
Finally, long term vision and impacts are related to the technological advances of DNA-FAIRYLIGHTS that will:
• make novel technologies available for new generation of data encoding and storage based on DNA
• significantly advance the field of biophotonics, plasmonics, and bio-inspired optoelectronics
• facilitate the development of new tools to characterize heterogeneous molecular ensembles through accurate and fast data reading based on optical readouts with the major advantage to avoid the need for random access.
In general, in the 2nd part of the project we expect more impactfull results. In particular, the highly interdisciplinary effort of DNA-FAIRYLIGHTS will lead to:
• development of advanced optical technologies based on NP and NC decorated (hybrid) DNA
• highly engineered systems for molecular functionalization
• Novel data encoding concepts based on multiplexed signals
• robust optical spectroscopic platform for single molecule reading based on solid-state nanopore arrays
• integration of the above technologies within a core multifunctional platform and
• iterative refinement of the data analysis based on assessment of instrument performance.
Finally, long term vision and impacts are related to the technological advances of DNA-FAIRYLIGHTS that will:
• make novel technologies available for new generation of data encoding and storage based on DNA
• significantly advance the field of biophotonics, plasmonics, and bio-inspired optoelectronics
• facilitate the development of new tools to characterize heterogeneous molecular ensembles through accurate and fast data reading based on optical readouts with the major advantage to avoid the need for random access.